Topoisomerase



Topoisomerase (TOP) winds and unwinds DNA double helix in order to enable DNA replication. TOPI cuts one strand of the double helix. It has 3 subclasses: TOPIA which shares its mechanism with TOPII and TOPIB which uses rotary mechanism and includes topo I and topo III. TOPIC called TOPV shares its mechanism with TOPIB but is structurally unique. TOPII cuts both strands of the double helix. Its subclasses are TOPIIA including topo II and TOPIIB which includes topo VI. TOPIV which is a type of TOPII, contains an ATP-binding domain ParE and a catalytic domain ParC. The images at the left and at the right correspond to one representative TOP, i.e. the crystal structure of Deinococcus radiodurans topoisomerase IB (2f4q).

3D Structures of Topoisomerase
Update June 2011

TOPI
3igc, 2h7f, 2h7g – TOPI+DNA – Smallpox virus

2gai, 2gaj – TOPI – Thermotoga maritime

2f4q – TOPIB – Deinococcus radiodurans

1tl8, 1sc7 – hTOPI+DNA+indenoisoquinoline – human

1seu - hTOPI+DNA+indolocarbazole

1t8i, 1rr8, 1rrj - hTOPI+DNA+camptothesin

1r49 – hTOPI (mutant)

1mw8 – hTOPI (mutant) N-terminal+DNA

1mw9 - hTOPI (mutant) N-terminal

1nh3 – hTOPI C-terminal+DNA+Ara-C

1k4s, 1lpq, 1ej9, 1a31, 1a35, 1a36 – hTOPI+DNA

1k4t - hTOPI+DNA+topotecan

1cy0 – EcTOPI+DNA - Escherichia coli

3px7 – EcTOPI (mutant) +DNA

1cy2, 1cy1 – EcTOPI+5’TPTPTP3’

1cy6, 1cy7, 1cy8 – EcIOPI+TMP

1cy9, 1cyy – EcTOPI domain II+III

1yua – EcTOPI C-terminal

1ecl, 1cy4 - EcTOPI N-terminal

3pwt - EcTOPIA N-terminal (mutant)

1a41 – VvTOPI C-terminal – Vaccinia virus

1vcc – VvTOPI N-terminal

1ois – yTOPI N-terminal - yeast

TOPIIA
3l4j – yTOPII apo+DNA

3l4k - yTOPII+DNA+Zn

2rgr - yTOPIIA+DNA

1qzr – yTOPII N-terminal+dexrazoxane

1pvg – yTOPII N-terminal

1bjt, 1bgw – yTOPII core

3ksa, 2ksb – SpTOPIIA+DNA – Streptococcus pneumoniae

1zxm – hTOPIIA+AMP-PNP

1zxn - hTOPIIA+ADP 3kua – TOPII residues 362-493 + CCDB – Vibrio fischeri

TOPIIB topo VI
2zbk – SsTOPIIB subunit A+B – Sulfolobus shibatae

2hkj, 1mu5, 1mx0 - SsTOPIIB subunit B

1z59, 1z5a - SsTOPIIB subunit B+ADP

1z5b - SsTOPIIB subunit B+ADP+AlF4

1z5c - SsTOPIIB subunit B+ADP+Pi

2q2e - TOPIIB subunit A+B – Methanosarcina mazei

1d3y - TOPIIB subunit A - Methanocaldococcus janaschii

TOPIII
2o19, 2o54, 2o59, 2o5c, 2o5e, 1i7d – EcTOPIII+DNA

1d6m - EcTOPIII

TOPIV
3fv5 – EcTOPIV subunit B

1zvt, 1zvu - EcTOPIV subunit A

1s14 – EcTOPIV ParE

1s16 - EcTOPIV ParE+ADPNP

3ltn, 3k9f, 3ksb - SpTOPIV subunit A+B+DNA

3foe, 3fof - SpTOPIV subunit A+B+DNA+quinolone

2nov - SpTOPIV subunit A

2inr - TOPIV subunit A – Staphylococcus aureus

1wp5 – TOPIV C-terminal – Geobacillus stearothermophilus 2xkj – AbTOPIV pare+parc subunits – Acinetobacter baumannii

2xkk - AbTOPIV pare+parc subunits+DNA

3lnu, 3lps - TOPIV subunit B N-terminal – Xanthomonas oryzae

TOPV
2csb, 2csd – TOPV – Methanopyrus kandleri

3m6k, 3m7g – MkTOPV N-terminal

3m6z - MkTOPV N-terminal+guanidine

3m7d - MkTOPV N-terminal+dioxane